#!/bin/bash

#time GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_A-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_A-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_B-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_B-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_C-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_C-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50814-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_A-NS50812.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50814-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_none_A-NS50814.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_24hr_2018.SW13_none.union_junctions.bed
#exit;

echo 1;
GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_tet_A-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_tet_A-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_tet_B-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_tet_B-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_tet_C-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/SW13_tet_C-NS50729.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_24hr_2018.SW13_tet.union_junctions.bed
echo 2;
GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_A-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_A-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_B-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_B-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_C-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_C-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50814-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_A-NS50812.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50814-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_none_A-NS50814.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_24hr_2018.iBRG1_none.union_junctions.bed
echo 3;
GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_tet_A-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_tet_A-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_tet_B-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_tet_B-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_tet_C-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iBRG1_tet_C-NS50729.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_24hr_2018.iBRG1_tet.union_junctions.bed
echo 4;
GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_A-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_A-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_B-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_B-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_C-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_C-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50814-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_A-NS50812.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50814-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_none_A-NS50814.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_24hr_2018.iHSA_none.union_junctions.bed
echo 5;
GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_tet_A-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_tet_A-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_tet_B-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_tet_B-NS50729.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_tet_C-NS50728.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50728-Archer-Dietrich/rnaseqProcessing/rnaseqOutput_v27lift37/iHSA_tet_C-NS50729.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_24hr_2018.iHSA_tet.union_junctions.bed
echo 6;
GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50955-Archer-Dietrich/rnaseq_processing/rnaseqOutput_v28lift37/NS50955.BRG-B.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50955-Archer-Dietrich/rnaseq_processing/rnaseqOutput_v28lift37/NS50955.BRG1-A.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_48hr_2019.iBRG1_none.union_junctions.bed
echo 7;
GENOME=hg19 /ddn/gs1/home/wardjm/Builds/NIEHS_IntegrativeBIx-svn/Bpipe/bpipeScripts/combJunc2bed12.sh /ddn/gs1/project/nextgen/post/archer1/NS50955-Archer-Dietrich/rnaseq_processing/rnaseqOutput_v28lift37/NS50955.BRG-tet-A.STAR_hg19.junctionsBed /ddn/gs1/project/nextgen/post/archer1/NS50955-Archer-Dietrich/rnaseq_processing/rnaseqOutput_v28lift37/NS50955.BRG-tet-B.STAR_hg19.junctionsBed > /data/wade/archerHubs/dietrichHub/hg19/union_files/BRG_48hr_2019.iBRG1_tet.union_junctions.bed